Draft talk:List of proteins in the human body

Trying to make a framework in which we can bind several categories and articles together

Varies wiki categories and articles have tried to list some of these proteins(Category:Human proteins, List of proteins,Category:Proteins, List of enzymes). But none of them have put them on a table form with a naming convention. This is an attampt at doing excatly that, establishing a sortable table with a naming convention, that people can easily add more of the 10 000 estimated human proteins, or sort the list depening on thier needs. Claes Lindhardt (talk) 12:39, 12 July 2023 (UTC)

As well as the contents of https://en.wikipedia.org/wiki/Index_of_protein-related_articles Claes Lindhardt (talk) 18:43, 12 July 2023 (UTC)

Transporter Classification Database could also be relevant? Claes Lindhardt (talk) 17:39, 18 July 2023 (UTC)

as well as: en.wikipedia.org/wiki/Proteins_produced_and_secreted_by_the_liver Claes Lindhardt (talk) 17:42, 18 July 2023 (UTC)

as well as: Actin-binding protein Claes Lindhardt (talk) 12:58, 22 July 2023 (UTC)

What is the difference?

what is the difference on Human Protein Reference Database and Human Proteinpedia they seem to be very related? Claes Lindhardt (talk) 18:58, 12 July 2023 (UTC)

Is there already some kind of convention for what types of proteins there is?

Chaperone (protein) is a kind of protein that we have not included yet, but which it seems like it might make sense to include as a type of protein in such a list. Is there already someone who have tried to make some kind of convntion for protein types? Claes Lindhardt (talk) 19:04, 12 July 2023 (UTC)

There seems to be pleanty of conventions for how to name proteins: i. e: https://www.ncbi.nlm.nih.gov/genome/doc/internatprot_nomenguide/, https://iubmb.qmul.ac.uk/proteinName.html, https://www.biosciencewriters.com/Guidelines-for-Formatting-Gene-and-Protein-Names.aspx, https://academic.oup.com/molehr/pages/Gene_And_Protein_Nomenclature, https://peakproteins.com/wp-content/uploads/2022/06/PPP_Protein-Construct-Naming-Convention.pdf, https://www.uniprot.org/help/protein_names, https://www.pnas.org/doi/10.1073/pnas.2025207118, https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/gene-nomenclature But is there any convention or guideline for the more general grouping of Human Proteins? or like types of Human Proteins Claes Lindhardt (talk) 19:11, 12 July 2023 (UTC)

this kind of goes in that direction: Protein family but not all the way Claes Lindhardt (talk) 17:44, 15 July 2023 (UTC)

Smartest way to represent the Amino Acid chain linked to a given protein

Would it make sense to make a column for the proteins amino Acid code? or is it better to just keep it as it is now where people can click the name to find the sequence, or would we want to also be able to sort all the human proteins based on thier Amino acid sequence? Claes Lindhardt (talk) 20:00, 12 July 2023 (UTC)

Automaising the maintaince of the article

Once all the proteins already on wiki is listed, I considered copyint the table into excel and then using something like: https://www.youtube.com/watch?v=_YMS74ZIPVs&ab_channel=GregAnderson or https://www.youtube.com/watch?v=0X6NxRDzMDQ&ab_channel=Excel%2CWordandPowerPointTutorialsfromHowtech to then make a script either directly in SQL or with Python that automatically checks for dublicates(to some degree) and overlabs. So that one can have a list of merge conflicts that one can resolve one by one. Does anyone know if there is already a tool for this on wiki. So that you woulden't have to first bring the data outside of wiki? and if maybe there is someone who have already made a such script for another wiki project? that one could re-use or take inspiration from? Claes Lindhardt (talk) 07:10, 19 July 2023 (UTC)

Protein Precusores?

To what degree should protein precursers be included? Should we make a column for all proteins where you can see its precusores? Claes Lindhardt (talk) 08:59, 19 July 2023 (UTC)

In my mind it would be ideal to have this included in the list. As it would make it easy to map which proteins have common ancistors and what we need to make what proteins Claes Lindhardt (talk) 09:23, 19 July 2023 (UTC)

Genes coding for proteins

Should the gene coding for each protein? or the protein sequence have its own colum? and how would it ideally be formatted? Claes Lindhardt (talk) 08:59, 19 July 2023 (UTC)

In my mind this would be nice to have for many of the same reasons as listed with the Protein Precusores Claes Lindhardt (talk) 09:24, 19 July 2023 (UTC)

Proteins which are none native to the human body, but which still works as medicine

Should pharmaceutical proteins which works with and in the the human body, but which are not native to the human body be included in this list? Claes Lindhardt (talk) 09:22, 19 July 2023 (UTC)

I guess medicine is a misleading word here, as one could make the argument that medicine is just another kind of food, and most things that we eat are native to the human body. - is there a smart way to address this without diving to deep into an epistological and ontological discussion on what it means that something is native to the human body? Claes Lindhardt (talk) 09:26, 19 July 2023 (UTC)

List of current dublicates for merging:

XCR1, Xanthine oxidase, Vascular endothelial growth factor Claes Lindhardt (talk) 10:08, 19 July 2023 (UTC)

Column with other species in which the same proteins are present(or good animal model candidates?)

would it make sense to have a such column? Claes Lindhardt (talk) 13:04, 22 July 2023 (UTC)

more intuitive way to make clear or visualize how much have been mapped vs. How much there is left to map?

Is there a better way to show how many proteins are listed here vs. how many we think there is vs. how many have been observed and described? Claes Lindhardt (talk) 13:05, 22 July 2023 (UTC)